For most medical practices with fewer than 50 employees, Gusto is the best payroll software in 2026: it automates multi-rate pay for clinical staff, files federal and state taxes automatically, and handles benefits in the same system. Larger practices and multi-location groups should look at Paylocity, which adds deeper HR, scheduling, and compliance tooling. If you want the lowest cost with live support, OnPay is the value pick.
Some links on this page may earn us a commission at no cost to you. We only recommend tools we use with clients.
Why payroll is different for a medical practice
Payroll in a clinic or med spa is messier than in a typical small business, and the software you pick needs to handle that mess without manual spreadsheets.
- Mixed pay types. Front desk staff are hourly, hygienists or nurses may have shift differentials, associates are often salary plus production bonus, and injectors in a med spa frequently earn commission on services sold. Your payroll system needs to run all of these in one pay cycle.
- Overtime exposure. Hourly clinical staff who cover for each other rack up overtime fast. You want automatic overtime calculation tied to actual time tracking, not a manager's memory.
- Credential-linked compliance. Some states tie pay rules to licensure and role. A system with role-based records keeps that paperwork in one place.
- Benefits expectations. Health coverage and retirement plans are standard recruiting tools for clinical talent. Payroll software that administers benefits in the same place saves hours every open enrollment.
If your practice still runs payroll by hand or through an accountant's spreadsheet, you are spending 3 to 6 hours per pay period that software does in minutes, and you carry all the tax filing risk yourself.
The top picks for 2026
Gusto: best for practices under 50 employees
Gusto hits the sweet spot for independent practices, dental offices, and med spas. Full-service payroll runs in a few clicks, taxes are filed automatically in all 50 states, and employees onboard themselves through their own portal, which matters when you hire a new front desk person every few months. Health insurance, 401(k), and workers' comp all live in the same dashboard. Pricing starts around $49 per month plus $6 per person, so a 12-person practice pays roughly $120 per month.
The main limitation: Gusto is payroll-first software. If you need serious scheduling, applicant tracking, or performance management, you will outgrow it.
Paylocity: best for larger or multi-location groups
Paylocity is a full human capital management platform: payroll plus scheduling, time and attendance, recruiting, onboarding, learning management, and compliance reporting. For a group with 50 or more employees across multiple locations, that consolidation is worth the higher price and the sales-call buying process. Practice managers particularly like the scheduling module for coordinating clinical coverage across sites.
OnPay: best value with live support
OnPay charges one flat rate (around $40 per month plus $6 per person) with no feature tiers, and its support team actually picks up the phone. It handles multiple pay rates, unlimited pay runs, and all tax filings. It has fewer integrations than Gusto, but for a lean practice that wants payroll done correctly and cheaply, it is hard to beat.
ADP Run: best if your accountant already lives in ADP
ADP Run is the safe, established choice, and many accounting firms work in ADP by default. Pricing is quote-based and usually lands higher than Gusto or OnPay for the same headcount, but if your CPA already manages clients in ADP, staying in that ecosystem reduces friction at tax time.
How to actually decide
- Count your employees and locations. Under 50 in one or two locations: Gusto or OnPay. Over 50 or three-plus locations: Paylocity or ADP.
- List your pay structures. Write down every pay type you run: hourly, salary, commission, production bonus, shift differential. Confirm the vendor supports each one natively before you sign.
- Check state coverage. If you employ remote billers or telehealth staff in other states, confirm the platform files in every state you touch.
- Ask about benefits administration. If you offer or plan to offer health insurance and a 401(k), keeping them inside payroll saves real administrative time.
- Run the switch at a quarter boundary. Migrating January 1 is cleanest; April, July, or October 1 are next best. Mid-quarter switches create messy partial-quarter tax filings.
What it costs to get this wrong
The IRS assessed billions in payroll tax penalties last year, and small employers who file manually carry most of that risk. A single late or incorrect 941 filing can cost more than a year of payroll software. Beyond penalties, practices that run payroll manually consistently underbill for the owner's time: 4 hours per pay period at a practice owner's effective hourly rate is thousands of dollars per year spent on data entry.
Modern payroll platforms take on tax filing liability for calculations made on their watch, automate new-hire reporting, and keep your records audit-ready. That is the real product: not the pay run, but the risk transfer.
Frequently Asked Questions
Can payroll software handle commission for med spa injectors?
Yes. Gusto, OnPay, and Paylocity all support commission and bonus pay types alongside hourly and salary in the same pay run. You enter or import the commission amounts each cycle, and the platform handles withholding correctly. If commissions come from your booking software, check for a direct integration or a CSV import.
Do I need HIPAA-compliant payroll software?
Payroll data itself (names, pay rates, hours) is not protected health information, so HIPAA does not apply to the payroll system in the way it applies to your EHR. You still want SOC 2 certified vendors with two-factor authentication, which all four platforms above provide.
How long does switching payroll providers take?
For a practice under 50 employees, plan on two to four weeks: one week to export records and set up the new account, one pay cycle running parallel checks, then cutover. The new provider's migration team does most of the data entry. Switching at a quarter start keeps tax filings clean.
Should my accountant run payroll instead?
If your accountant uses modern software and charges a flat fee, that can work fine. The problem is usually speed and self-service: employees cannot pull their own pay stubs or W-2s, and off-cycle runs (a missed bonus, a final paycheck) take days instead of minutes. Most practices are better off running software in-house and giving the accountant reporting access.
Written by Matthew Garcia. Last updated July 14, 2026. Questions? Email info@srtagency.com.